Using genomics: especially for pig health

Using genomics: especially for pig health Graham Plastow University of Alberta NSIF Annual Meeting Lincoln, NE December 2011

What is Genomics? The study of the genome: genes and variation in DNA sequence Closely related to a series of omics, e.g. transcriptomics (gene expression) proteomics.

What is Genomics? The study of genes (variation in DNA sequence) In animals, in order to be able to explain variation in economically important traits So as to improve our ability to select sires, dams, matings, animals in order to optimize processes and products Requires genomic tools but also data..

Why Genomics? Parentage or the origin of a piece of meat To identify carriers of a genetic disease To manage genetic health /diversity (df) To determine the genetic potential of an animal at birth E.g. The carcass grade of a steer/sl. pig A sire s ability to breed prolific daughters An animals ability to tolerate environmental or disease challenge (robustness)

1 2 3 4 Potential gains from MAS Meuwissen & Goddard, 1996 QTL with 1/3 of genetic variance haplotype-marked h 2 =.27 70 64 62 60 50 40 30 38 38 30 37 25 31 55 21 39 Provided by Jack Dekkers (ISU) 20 10 0 9 5 4 1 2 3 Generation 5 2 15 Meat Quality Litter Size Performance after selection Performance before selection

Genomics Catch 22 Genomics requires lots of data Adds real value for difficult or expensive to measure traits Where do we have lots of data? For easy to measure traits (& dairy bulls) So, we develop markers for easy to measure traits These markers have a relatively small impact (except for dairy)

Genomics Catch 22 Genomics requires lots of data Adds real value for difficult or expensive to measure traits Where do we have The lots of data? For easy to measure traits (& dairy bulls) Phenomic So, we develop markers for easy to measure traits Gap These markers have a relatively small impact (except for dairy)

Application of Genomics in Animals Marker Assisted Selection (MAS/GAS) To determine the genetic potential of an animal at birth Marker Assisted Management (MAM) To help optimize production/return by sorting animals into treatment groups Genome Wide Association Studies (GWAS) Genomic Selection

Take-home Genomics can help add value throughout the chain (MAM as well as MAS) State-of-the-art genomics tools are available now! Their greatest value is to impact difficult/expensive to measure traits Need to work with large numbers which means working with commercial animals Requires sharing information between participants

Today is the age of Genome Sequence

Cost of sequencing The human genome sequence, the culmination of 13 years effort and an estimated $3 billion was completed in 2003. Early in 2009, the first cow sequence was completed at $50 million in 4 years. The sequence of the two Canadian bulls took around 7 months at a cost of $130,000. Current Gentec Cost <$20,000 per individual (up to 100x)

Costs reduce faster than Moore s law Allows us to consider direct approaches We don t need the genetic proofs before we ask with today s genomics Of course it s harder for most diseases or complex traits Even so we still see the unexpected

Genomic Tools Today High Density SNP Chips allow Whole Genome Association Analysis Genomic Selection The Pig Genome Sequence enables Rapid identification of SNPs Fine mapping Analysis of other types of variation Characterization of genes and pathways (RNAseq)

Genomics of Swine Health: an example of a Canada-wide Livestock Gentec initiative.

Breeding for Disease Resistance Or reduced susceptibility Host Genetic Variation Identified For every type of pathogen Probably exists for all diseases Major opportunity for genomics As difficult and expensive to measure trait May be only practical way to breed healthier pigs Specific diseases or Improved Robustness?

1 2 3 4 The Phenomic Roadblock The real benefit will be from addressing 70 difficult to measure 60 traits 50 40 Significant efforts are 30 needed to measure 20 these traits on 10 sufficiently large 0 numbers of animals. 9 38 64 38 30 5 37 62 4 25 31 55 2 15 21 39

Health is the Biggest Opportunity for Genomics It represents an opportunity for the Canadian swine industry to build on its reputation for healthy genetics

Application of genomics to improve swine health and welfare An international industry/research partnership Project Leaders: Graham Plastow (UofA), John Harding (UofS), Bob Kemp (PigGen Canada)

Objective To provide new diagnostic tools to select for pigs that are genetically less susceptible to PCVAD and PRRS PCVAD - Porcine Circovirus Associated Disease PRRS Porcine Reproductive and Respiratory Syndrome Virus 21

How? By creating extensive resources for an integrated genomic analysis (and banking for future analysis) of host/virus interaction By integrating the research with application through use of industry populations, management and environments, and GE 3 LS enablement 22

The Need (Canadian Swine Health Forum Oct 2010) PRRS in Canada Very costly - in excess of $130 million/year in Canada PCVAD in Canada Total Direct Impact $500M plus on-going cost to cure of $600M 23

Global impact US: Because of PRRS, pig producers are known to suffer an estimated loss of $700 million a year. Neumann, E.J., et al. (2005) Assessment of the economic impact of porcine reproductive and respiratory syndrome on swine production in the United States. Journal of the American Veterinary Medical Association 227: 385-392. so-called high fever disease in China in 2006 with the essence of PRRS, which spread to more than 10 provinces (autonomous cities or regions) and affected over 2,000,000 pigs with about 400,000 fatal cases. K. Tian et al. PLoS ONE. 2007; 2(6): e526. Emergence of Fatal PRRSV Variants: Unparalleled Outbreaks of Atypical PRRS in China and Molecular Dissection of the Unique Hallmark

A Coordinated effort PigGen Canada Livestock Gentec US PRRS Host Genetics Consortium Genome Alberta/ALMA Applied Livestock Genomics Program Genome Canada Large-Scale Applied Research Project Competition (PRRSv/PVC2) Canadian Swine Health Board..

A Coordinated effort PigGen Canada Livestock Gentec US PRRS Host Genetics Consortium $9.3M new funding Genome Alberta/ALMA Applied Livestock Genomics Program >$5M PHGC Genome Canada Large-Scale Applied Research Project Competition (PRRSv/PVC2) Canadian Swine Health Board.. >$1M other co-funding

Coordinated effort Phalanx of phenomic/genomic tests Blood for r/t window on health Serum components In vitro tests (proliferation assays, MDMs, transcriptomics.) Post-hoc analyses (transcriptomics, proteomics, kinomics) Genotype Dedicated pool of experts/analysts (across models) Linked animal resources providing discovery, validation, calibration, and demonstration Banked samples providing options for new tests/hypothesis testing

The PRRS Host Genetics Consortium PHGC Understanding the role of host genetics in resistance to PRRSV infection, and the effects of PRRS on pig health and related growth. Uses a nursery pig model to assess pig resistance/ susceptibility to primary PRRSV infection. 1600 crossbred pigs (PIC USA; Newsham Choice Genetics; Fast Genetics; Genetiporc; Genesus). After acclimation, pigs infected with PRRSV and followed for 42 days post infection (dpi). Blood samples collected at 0, 4, 7, 10, 14, 21, 28, 35 and 42 dpi, and weekly weights recorded. Results have affirmed that all pigs become PRRSV. Multivariate statistical analyses of viral load and weight data have identified PHGC pigs in different virus/weight categories. Sera are now being compared for factors involved in recovery from infection, including speed of response and levels of immune cytokines. Overall, the PHGC project will enable researchers to verify important genotypes and phenotypes that predict resistance/susceptibility to PRRSV infection.

PHGC Phenotypes

PHGC Phenotypes HvLg HvHg LvLg LvHg

Why PRRS? $700 million/yr in US Weight distribution at different times after infection Number Weight

Results for GWA study using 60K chip Jack Dekkers and Nick Boddicker

The Partnership Agricultural Research Service University of Lincoln- Nebraska 34

PRRS Host Genetics Consortium (PHGC) PIs: Joan Lunney (USDA BARC) and Bob Rowland (Kansas State University) 1,600 growing pigs challenged with PRRSV strain 1 1,000 growing pigs challenged with PRRSV strain 2 PCV2 Host Genetics Consortium PI: Daniel Ciobanu (University of Nebraska) 400 growing pigs challenged with PCV2 600 growing pigs challenged with PCV2 S a m p l e s PI: Jim Reecy (Iowa State University) Project Database Project Database PI: Paul Stothard (University of Alberta) 2,000 animals 2,000 animals 300 Microarrays & 165 RNAseq 60k Porcine SNP Chip Transcriptomics 400 RNAseq Gilt Acclimation in Commercial Farms CSHB & PigGen Canada PI: Bob Kemp (PigGen Canada) 4,000 gilts introduced into low health status farms a n d FMIA Assays Kinomics 1,000 assays FMIA Assays Performance of 4,000 sows in low health status farms (from gilts above) Genome Canada Pregnant Gilt Challenge Model PI: John Harding (University of Saskatchewan) 120 pregnant gilts challenged with PRRSV (plus 20 in pilot trials) & approx. 1,000 fetuses D a t a In Vitro Assays Macrophage/PMBC Stimulation APPLICATIONS GWAS Identification of DNA Marker Panels Genes & Pathway Analysis Identification of Targets Calculation of GEBVs Colours indicate funding sources

400 growing pigs challenged with PCV2 600 growing pigs challenged with PCV2 Gilt Acclimation in Commercial Farms CSHB & PigGen Canada PI: Bob Kemp (PigGen Canada) 4,000 gilts introduced into low health status farms Thanks! Performance of 4,000 sows in low health status farms (from gilts above) Genome Canada Pregnant Gilt Challenge Model PI: John Harding (University of Saskatchewan) 120 pregnant gilts challenged with PRRSV (plus 20 in pilot trials) & approx. 1,000 fetuses e s a n d D a t a

S a m p l e s PI: Jim Reecy (Iowa State University) Project Database Project Database Thanks! PI: Paul Stothard (University of Alberta) 2,000 animals 2,000 animals 300 Microarrays & 165 RNAseq 60k Porcine SNP Chip Transcriptomics 400 RNAseq a FMIA Assays FMIA Assays

s a n d FMIA Assays Kinomics 1,000 assays FMIA Assays D a t a In Vitro Assays Macrophage/PMBC Stimulation APPLICATIONS GWAS Identification of DNA Marker Panels Genes & Pathway Analysis Identification of Targets Calculation of GEBVs Colours indicate funding sources

New phenotypes? Yes, but how? Can we use high throughput genomics as a tool to solve phenotypes as well?

New genomics approaches molecular phenotyping Leroy Hood, Institute for Systems Biology PAG Plenary Lecture 12 Jan 2009 Blood, a window into health and disease Organ-specific blood biomarkers Early disease diagnostics, stratification, progression Assessing treatment response (in individuals) wellness assessment (longitudinal, individual is own control)

New genomics approaches Chris Tuggle, ISU PAG Swine workshop 2009 PAG 641...expressed gene sets in...whole blood in response to infection with Salmonella Gene expression analysis of blood during early infection will identify genes important for classifying response between low shedders and persistent shedding pigs Predictors?

Success Factors Leadership shared vision Collaboration Industry Government Academic National and International Recipe Genotype + phenotype = information

Thanks!